Resolution:
standard / ## Figure 7.
Additive profiles. The profile functions in MUSCLE require amino acid frequencies for each column. Here
we show the alignment of two profiles X and Y, giving a new profile Z. Note that the
count n^{Z}_{i }for amino acid i in a given column of Z is the sum of the counts in the child profiles, i.e. n^{Z}_{i }= n^{X}_{i }+ n^{Y}_{i}. In terms of frequencies, this becomes f ^{Z}_{i }= N^{X}f ^{X}_{i }/N^{Z }+ N^{Y}f ^{Y}_{i}/N^{Z}, where N^{X}, N^{Y}, N^{Z }are the number of sequences in X, Y and Z respectively. Therefore, given a suitable
sequence weighting scheme, it is possible to compute frequencies in Z from the frequencies
in X and Y. This avoids the step of building an explicit multiple alignment for Z
in order to compute frequencies, as done in CLUSTALW and MAFFT.
Edgar |